Maybe run a virtual machine and plunk the server inside it. Just get a very lightweight linux, put it in Hyper-V or VirtualBox if you don't have Pro, and there you go. Separated and containerfied.
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That could be another option, but seriously, is there no way to prevent Windows from automatically logging out idle users?
Can you run the application as a service as opposed to via a user account?
The server is being run from a batch script (command prompt) and then has a java applet running alongside it, but I don't want it to be running through my main account (hence the separation).
The way it's been working out has been great, but this logging out business needs to stop. LOL
Not the best security practice but to answer you question, there is likely a policy setting in the registry or via policy you could change. This one should be set to 0. You could also maybe run a program of some sort via task scheduler as a workaround (to mimic mouse/keyboard input via autohotkey or using a "keep PC awake" variable? This also has better suggestions. If it's logging off while you're not using the PC, it may be that the computer is entering a sleep state.
Thank you! I think the Interactive logon machine setting might be what I'm looking for. The machine is actually in use quite often and all sleep/screensaver options have been disabled (It's a mini-PC hooked up to a TV, so it acts as our multimedia device while running the minecraft server in the second account.